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| Status |
Public on Jul 03, 2024 |
| Title |
GBM3, Patient3, Region4 |
| Sample type |
SRA |
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| Source name |
WHO Grade IV GBM
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| Organism |
Homo sapiens |
| Characteristics |
tissue: WHO Grade IV GBM
subject id: Patient3
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| Extracted molecule |
total RNA |
| Extraction protocol |
For ST sequencing, 16 fresh tissue samples were extracted via surgery from 3 glioblastoma patients. The GBM tumor specimens were promptly frozen in liquid nitrogen and embedded in OCT compound. The frozen tissue specimens were then cryo-sectioned at a thickness of 10 µm and were mounted on pre-treated glass slides and incubated at 37°C for 1 minute , followed by fixation in methanol for 30 min at -20°C and washing in phosphate buffered saline. The current ST protocol was applied to all sections, resulting in both conventional hematoxylin and eosin (H&E) images that were amenable to annotation by pathologists, as well as gene expression profiles for each microarray spot.
Spatial Transcriptomome sequencing libraries were prepared with 10 × Genomics Visium Spatial Gene Expression Slides & Reagent Kit according to manufacturer's construction
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
GBM3-R4_D
Fresh frozen Spatial transcriptome sequencing
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| Data processing |
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10 × Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding gene were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_oimage.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
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| Submission date |
Jan 11, 2024 |
| Last update date |
Jul 03, 2024 |
| Contact name |
xuejiao lv |
| E-mail(s) |
xuejiaolv28@tmu.edu.cn
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| Phone |
18322664803
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| Organization name |
Tianjin Medical University
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| Street address |
No.22 Qixiangtai Rd
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| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE253080 |
Decoding Heterogeneous and Coordinated Tissue Architecture in Glioblastoma Using Spatial Transcriptomics |
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| Relations |
| BioSample |
SAMN39412375 |
| SRA |
SRX23171620 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8013410_GBM3-R4_aligned_fiducials.jpg.gz |
2.1 Mb |
(ftp)(http) |
JPG |
| GSM8013410_GBM3-R4_barcodes.tsv.gz |
19.9 Kb |
(ftp)(http) |
TSV |
| GSM8013410_GBM3-R4_detected_tissue_image.jpg.gz |
2.2 Mb |
(ftp)(http) |
JPG |
| GSM8013410_GBM3-R4_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM8013410_GBM3-R4_matrix.mtx.gz |
41.2 Mb |
(ftp)(http) |
MTX |
| GSM8013410_GBM3-R4_scalefactors_json.json.gz |
174 b |
(ftp)(http) |
JSON |
| GSM8013410_GBM3-R4_tissue_hires_image.png.gz |
6.0 Mb |
(ftp)(http) |
PNG |
| GSM8013410_GBM3-R4_tissue_lowres_image.png.gz |
630.0 Kb |
(ftp)(http) |
PNG |
| GSM8013410_GBM3-R4_tissue_positions_list.csv.gz |
59.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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